Merge pull request #169 from wtsi-npg/devel

Pull from devel to master to create release 52.2.5
wtsi-npg · Nov 29, 2024 · 9e7ac6e · 9e7ac6e
2 parents 216f5ae + 0d28a17
commit 9e7ac6e
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Showing 3 changed files with 59 additions and 22 deletions.
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -11,12 +11,13 @@ jobs:
         shell: bash -l -e -o pipefail {0}
 
     env:
-      PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
-      NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
-      WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic"
+      PERL_CACHE: $HOME/perl5 # Perlbrew and CPAN modules installed here, cached
+      NPG_LIB: $HOME/perl5npg # NPG modules installed here, not cached
+      WSI_CONDA_CHANNEL: https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic
+      CONDA_HOME: $HOME/conda
       CONDA_TEST_ENV: test-environment
       WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
-      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF}
+      WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
 
     strategy:
       matrix:
@@ -34,31 +35,31 @@ jobs:
           sudo apt-get remove -y nginx libgd3
           sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl
 
-      - name: "Initialize Miniconda"
+      - name: "Install Miniforge"
         run: |
-          echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile"
+          CONDA_HOME=${{ env.CONDA_HOME }} ./scripts/install_miniforge.sh
+          echo 'source "${{ env.CONDA_HOME }}/etc/profile.d/conda.sh"' >> "$HOME/.bash_profile"
 
       - name: "Cache Conda"
-        id: minicondaCache
+        id: miniforgeCache
         uses: actions/cache@v4
         with:
           path: |
-            ~/conda/pkgs
-            ~/conda/envs
-          key: ${{ runner.os }}-build-miniconda
+            ${{ env.CONDA_HOME }}/pkgs
+            ${{ env.CONDA_HOME }}/envs
+          key: ${{ runner.os }}-build-miniforge
 
       - name: "Install Conda packages"
         run: |
-          conda config --prepend pkgs_dirs ~/conda/pkgs
-          conda config --prepend envs_dirs ~/conda/envs
+          conda config --prepend pkgs_dirs ${{ env.CONDA_HOME }}/pkgs
+          conda config --prepend envs_dirs ${{ env.CONDA_HOME }}/envs
 
           conda config --set auto_update_conda False
-          conda config --prepend channels "$WSI_CONDA_CHANNEL"
-          conda config --append channels conda-forge
+          conda config --prepend channels "${{ env.WSI_CONDA_CHANNEL }}"
           conda info
 
-          conda create  -y -n "$CONDA_TEST_ENV"
-          conda install -y -n "$CONDA_TEST_ENV" biobambam2
+          conda create  -y -n "${{ env.CONDA_TEST_ENV }}"
+          conda install -y -n "${{ env.CONDA_TEST_ENV }}" biobambam2
 
       - name: "Cache Perl"
         id: cache-perl
@@ -88,12 +89,12 @@ jobs:
       - name: "Install Perl dependencies"
         run: |
           cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
-          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="${{ env.NPG_LIB }}")
           eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
           
           cpanm --quiet --notest Module::Build
           
-          ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
+          ./scripts/install_wsi_dependencies.sh "${{ env.NPG_LIB }}" \
              perl-dnap-utilities \
              ml_warehouse \
              npg_tracking
@@ -103,23 +104,23 @@ jobs:
       - name: "Log install failure"
         if: ${{ failure() }}
         run: |
-          find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
+          find $HOME/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
 
       - name: "Archive CPAN logs on failure"
         if: ${{ failure() }}
         uses: actions/upload-artifact@v4
         with:
           name: cpan_log
-          path: ~/.cpanm/work/*/build.log
+          path: $HOME/.cpanm/work/*/build.log
           retention-days: 5
 
       - name: "Run tests"
         run: |
-          conda activate "$CONDA_TEST_ENV"
+          conda activate "${{ env.CONDA_TEST_ENV }}"
           conda info --envs
           
           eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
-          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="${{ env.NPG_LIB }}")
           
           export TEST_AUTHOR=1
           perl Build.PL

diff --git a/Changes b/Changes
@@ -1,5 +1,8 @@
 LIST OF CHANGES
 
+release 52.2.5 (2024-11-29)
+ - replace miniconda with miniforge for CI
+
 release 52.2.4 (2024-10-04)
  - Added .github/dependabot.yml file to auto-update GitHub actions
  - Following a release on 07/09/2024, see https://metacpan.org/dist/App-perlbrew/changes

diff --git a/scripts/install_miniforge.sh b/scripts/install_miniforge.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+#
+# Once installed, the Conda environment can be activated by running:
+#
+# source $CONDA_HOME/etc/profile.d/conda.sh
+#
+# conda activate
+
+set -ex
+
+MINIFORGE_VERSION="24.9.0-0"
+MINIFORGE_SHA256="77fb505f6266ffa1b5d59604cf6ba25948627e908928cbff148813957b1c28af"
+
+CONDA_HOME=${CONDA_HOME:-"$HOME/conda"}
+export CONDA_HOME
+
+CONDARC="$HOME/.condarc"
+export CONDARC
+
+cat <<EOF > "$CONDARC"
+auto_update_conda: false
+always_yes: true
+ssl_verify: true
+show_channel_urls: true
+
+channels:
+  - conda-forge
+EOF
+
+curl -sSL "https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Mambaforge-${MINIFORGE_VERSION}-Linux-x86_64.sh" -o ./miniforge.sh
+sha256sum ./miniforge.sh | grep "$MINIFORGE_SHA256"
+/bin/bash ./miniforge.sh -b -p "$CONDA_HOME"
+rm ./miniforge.sh